title: C. gibelio, triploid, male, replicate_5

city: Brno

first: Andrea

middle: Vetešníková

last: Šimková

address: Kamenice 5

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

data_processing:
A quality check of raw paired-end fastq reads was carried out by FastQC and their origin was categorized using BioBloomTools v2.3.4. The Illumina adapters clipping and quality trimming of raw fastq reads were performed using Trimmomatic v0.39 with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35. Trimmed RNA-Seq reads were mapped to the reference genome using STAR v2.7.3a as a splice-aware short read aligner and default parameters except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic. Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools – namely, RSeQC v4.0.0, Picard toolkit v2.25.6, and Qualimap v.2.2.2. All statistics were processed by MultiQC v1.10.1.
The genomic sequences of all collected samples were aligned to the reference genome utilizing the Burrows-Wheeler Aligner (BWA) software. Post alignment and germline variants were called using Strelka2 variant calling software, generating variant calls in VCF format which were further filtered to retain only high-confidence variants. These variants were then annotated using the reference annotation in GTF file. Subsequent data processing was carried out in R, where the variant tables were further refined and merged with sample information. A series of filtering steps were performed to ensure only variants with sufficient coverage and sample counts were retained for analysis. The filtered variant table was then reorganized and formatted for subsequent comparative analyses. Variants located on sex chromosomes were excluded for certain analyses to ensure accurate cross-species comparisons. The data were then restructured to compare SNP identity across species, generating similarity matrices and Venn diagrams to visualize the overlap of SNPs by species and ploidy levels.
The differential gene expression was calculated on the basis of the gene counts produced using featureCounts from the Subread package v2.0 and further analysed by Bioconductor package DESeq2 v1.34.0. Data generated by DESeq2 with independent filtering were selected for differential gene expression analysis to avoid potential false positive results. Differences in gene expression were considered significant on the basis of a cut-off of the adjusted p-value ≤ 0.05. GO term enrichment was analysed using David to retrieve Gene Ontology terms in the Biological process, Cellular Component and Molecular function categories, as well as KEGG pathways. Graphical representations of the GO enrichment were realized using R and Revigo. Reproduction-associated candidate genes were retrieved using the BlastKoala tool of KEGG, the BioMart tool of Ensembl, and published studies. GO terms enrichment was tested using Fisher’s exact test (α = 0.05) with false discovery rate (FDR) correction of the p-value. To interpret the biological functions of the DEGs, their mapping to the Gene Ontology (GO) and KEGG databases was performed to analyse pathway enrichment. In each of six fish groups associated with sexual reproduction and asexual males, significantly differently-expressed genes (DEGs) compared to the triploid asexual females of C. gibelio were selected on the basis of the following criteria: Basemean > 10, and a padj value < 0.05,. For KEGG pathway analysis, no filtering based on log2 fold change was applied. Gene functions were investigated using the biological databases Uniprot, KEGG, Zfin and GeneCards. PCA was performed using the DESeq2 R package. For PCA based on reproduction-associated genes, a set of 208 reproduction genes was selected using the BioMart tool of Ensembl.
Assembly: Carassius auratus genome (ASM336829v1) with Ensembl annotation (release 104)
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

organism: Carassius gibelio

source_name: gonadal

growth_protocol: Asexual and sexual C. gibelio were obtained from artificial breeding. Asexual females were obtained by induced embryogenesis using sperm of C. carpio. The sexual specimens were obtained from the interbreeding of sexual specimens. The fish were reared in aquarium conditions until the age of four years and subsequently their gonadal tissues were sampled (the age of the examined fish corresponded to 4+). Cyprinus carpio and Carassius auratus were obtained from external breeding facilities. Four or five biological samples per fish group from a total of 8 fish groups were analysed (females and males of C. gibelio resulting from sexual reproduction, females and temperature-induced males of C. gibelio resulting from gynogenesis, females and males of sexual C. auratus, and females and males of sexual C. carpio).

extract_protocol:
Total RNA was isolated from the gonad tissue of each fish specimen. For extraction, PureLink® RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific) and on-column PureLink DNase treatment were used according to the manufacturer´s protocol. Reagent and buffer volumes were adjusted according to the weight of tissue entering the isolation process (30 mg on average). The final elution was performed using 100 µl of RNAse-free water in the first step and the primal eluate in the second step. The yield and concentration of RNA isolates were checked using a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) and Qubit RNA HS Assay Kit (Thermo Fisher Scientific). The quality and integrity of RNA were analysed using RNA 6000 Nano Kit on a 2100 Bioanalyser instrument (Agilent Technologies). All RNA isolates were normalized by dilution at a uniform concentration of 20 ng/µl with RNase-free water. They served as templates for DNA library preparation in twice the reaction volume recommended by the manufacturer.
All samples (RNA integrity number – RIN > 7) were used for DNA library preparation. 500ng of total RNA was used for mRNA enrichment using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®, and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) were used for library preparation, with 11 PCR cycles utilized for PCR enrichment. RNA fragmentation (13 minutes at 94°C) and the size selection conditions (a bead volume of 30 µl and 15 µl for the first and second bead selections, respectively) were further modified in the protocol. The quantification of DNA libraries was performed on a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) using Qubit dsDNA HS Assay Kit, and quality and size control were performed on a 2100 Bioanalyser with DNA 1000 Kit (Agilent Technologies). Finally, amplicons were pooled in equimolar amounts. The final concentration of each library in the pool was 10 nM in the pool. Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) together with spike-in RNA were used for cDNA library preparation from total RNA. The quality of prepared cDNA libraries was evaluated using a Qubit fluorometer (Thermo Fisher). The quality of cDNA libraries was visualized by a 2100 Bioanalyser (Agilent), and the libraries were were finally sequenced by Macrogen Korea on Illumina HiSeq X (one lane) in a paired-end configuration producing 150 bp long reads.

treatment_protocol: Gonadal tissues of each fish specimen were individually submerged in Ambion RNAlater stabilization solution (Thermo Fisher Scientific). Tubes with tissues were stored at -80ºC until the isolation of total RNA.

value: gonadal

tag: ploidy

value: triploid


title: nasal_epithelial_cell, 646d_40cc

status: Public on May 17 2024

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58th Street, CLSC 501

department: Human Genetics

country: USA

institute: The University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Asthma&Allergy Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using standard Illumina scanner settings.

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5%) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using ENmix. Please see https://github.com/hansenlab/IlluminaHumanMethylationAllergymanifest/tree/4a00cd62600a662f9a5f1cd32b5aeecee87225a8 for annotation and manifest packages.
MatrixProcessed.txt:  ENmix normalized Beta values
SignalIntensities.txt:  Unmethylated and methylated signal intensities after background normalization.

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol.

extract_protocol: Flocked nasal swabs were obtained at age 5-7 years and samples were stored at -80, then extracted using AllPrep DNA/RNA kit (Qiagen) following the manufacturer's protocol.

tag: Sex

value: female

tag: proportionpositiveskinpricktests

tag: plate

tag: ageindays

value: multiple

tag: cohort (the year of sample recruitment)

tag: array


title: nasal_epithelial_cell, 5891_42b9

value: male


title: C. gibelio, triploid, male, replicate_3

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: nasal_epithelial_cell, 4f70_455f

value: hispanic


title: nasal_epithelial_cell, 76a2_4756


title: C. gibelio, triploid, female, replicate_5


title: C. gibelio, triploid, male, replicate_2


title: C. gibelio, triploid, male, replicate_4


title: C. gibelio, triploid, female, replicate_3


title: nasal_epithelial_cell, 291c_4b05


title: nasal_epithelial_cell, 5ebf_4dc4


title: nasal_epithelial_cell, ca13_45cb


title: C. gibelio, triploid, female, replicate_2


title: nasal_epithelial_cell, c134_49ca


title: C. gibelio, triploid, female, replicate_1


title: C. gibelio, triploid, male, replicate_1


title: C. gibelio, diploid, male, replicate_5

value: diploid


title: C. gibelio, diploid, female, replicate_5


title: nasal_epithelial_cell, d8d7_4a4e


title: nasal_epithelial_cell, e16b_4743


title: nasal_epithelial_cell, 8f04_4418


title: C. gibelio, triploid, female, replicate_4


title: C. gibelio, diploid, female, replicate_4


title: C. gibelio, diploid, male, replicate_3


title: nasal_epithelial_cell, 042a_486a


title: C. gibelio, diploid, male, replicate_2


title: C. gibelio, diploid, female, replicate_3


title: nasal_epithelial_cell, 9448_40bd


title: C. gibelio, diploid, male, replicate_1


title: C. gibelio, diploid, female, replicate_2


title: nasal_epithelial_cell, 617d_4133


title: nasal_epithelial_cell, a9dc_4f9d


title: nasal_epithelial_cell, ce49_49c3


title: BCG Week 6 Post BCG 3' scRNAseq

city: New York

first: Michelle

middle: A

last: Tran

state: New York

address: 1470 Madison Ave

institute: Icahn School of Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v. 5.0.1 (https://www.10xgenomics.com/support/software/cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated value and matrix files

source_name: Urine

extract_protocol:
Urine cells were spun down from urine at 500g for 5 mins and filtered through a 70 uM filter. Tumor cells were received freshly from the surgical operating room immersed in RPMI 1640 media (11875-093; Gibco). Tumors were immediately minced and digested using an enzume cocktail from a Tumor Dissociation Kit (130-095-929; Miltenyi Biotec) and mechanical disociation with heat using the 37C_h_TDK_2 program on the gentleMACS (130-096-427, Miltenyi Biotec). Cells were then filtered through 100 μm, 70 μm, and 40 μm cell filters. Whole peripheral blood was spun at 300g for 7 minutes, and plasma was removed and frozen down. PBMCs were isolated by centrifugation over a Ficoll400 cell separation solution (17-1440-03; GE Healthcare) with red blood cells removed by ACK lysis buffer (A10492-01; Gibco).
Single-cell RNA sequencing was conducted on these samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3’ or 5’ gene expression (GEX) V3 kit (as indicated in the sample title). Gel-Bead in Emulsions (GEMs) were created on the sample chip in the Chromium controller, and barcoded cDNA was extracted by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing as per manufacturer’s protocols. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis.

value: Urine

tag: cell type

value: urine-derived cells


title: nasal_epithelial_cell, c832_4439


title: nasal_epithelial_cell, 9c48_4eb6


title: nasal_epithelial_cell, e64b_4eda


title: BCG Week 5 Post BCG 3' scRNAseq

description: 10X Genomics


title: BCG Week 6 Pre BCG 3' scRNAseq

description: 10X Genomics


title: BCG Week 5 Pre BCG 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 46fc_425e


title: nasal_epithelial_cell, 0c7e_466e


title: nasal_epithelial_cell, 3732_4e15


title: C. gibelio, diploid, male, replicate_4


title: nasal_epithelial_cell, b787_4ac1


title: BCG Week 3 Post BCG 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, ef25_44f9


title: nasal_epithelial_cell, b0cf_4b05


title: nasal_epithelial_cell, ed88_4ac3


title: BCG Week 3 Pre BCG 3' scRNAseq

description: 10X Genomics


title: BCG Week 1 Post BCG 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 1e86_442e


title: nasal_epithelial_cell, 20ba_458a


title: BCG Week 1 Pre BCG 3' scRNAseq

description: 10X Genomics


title: Patient 9 PBMC 3' scRNAseq

description: 10X Genomics

source_name: Peripheral blood

value: Peripheral blood

value: peripheral blood mononuclear cells


title: Patient 9 Urine 3' scRNAseq

description: 10X Genomics


title: C. gibelio, diploid, female, replicate_1


title: nasal_epithelial_cell, 54bf_44b3


title: nasal_epithelial_cell, a0b7_405d


title: nasal_epithelial_cell, 8a29_4a87


title: nasal_epithelial_cell, 48b0_441c


title: BCG Week 4 Post BCG 3' scRNAseq

description: 10X Genomics


title: Patient 8 Urine 3' scRNAseq

description: 10X Genomics


title: Patient 8 PBMC 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, c551_4516


title: nasal_epithelial_cell, 91ef_4906


title: Patient 7B Tumor 3' scRNAseq

description: 10X Genomics

source_name: Tumor

value: Tumor

value: tumor cells


title: nasal_epithelial_cell, f865_49de


title: Patient 7B Urine 3' scRNAseq

description: 10X Genomics


title: Patient 7A Tumor 3' scRNAseq

description: 10X Genomics


title: Patient 7A PBMC 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 5792_4447


title: Patient 7A Urine 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, f6cb_4038


title: Patient 6 Tumor 5' scRNAseq

description: 10X Genomics


title: Patient 9 Tumor 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, c66d_4cb9


title: nasal_epithelial_cell, 765c_4ee1


title: Patient 6 Urine 5' scRNAseq

description: 10X Genomics


title: Patient 6 PBMC 5' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 340b_4f18


title: Patient 8 Tumor 3' scRNAseq

description: 10X Genomics


title: Patient 5 PBMC 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 6746_467a


title: Patient 5 Urine 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 8128_4ce1


title: Patient 4 Tumor 5' scRNAseq

description: 10X Genomics

source_name: Bladder tumor

value: Bladder tumor


title: nasal_epithelial_cell, 18d9_4e07


title: Patient 5 Tumor 3' scRNAseq

description: 10X Genomics


title: Patient 4 Urine 5' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 4257_4507


title: nasal_epithelial_cell, d5c5_4e96


title: nasal_epithelial_cell, c570_46a4


title: Patient 3 Urine 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 757a_426b


title: Patient 2 Tumor 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 9167_4387


title: Patient 3 Tumor 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 638b_47f5


title: nasal_epithelial_cell, a8c8_406c


title: Patient 2 Urine 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, ea60_445c


title: nasal_epithelial_cell, eb17_4ef1


title: Patient 1 Urine 3' scRNAseq

description: 10X Genomics


title: nasal_epithelial_cell, 7805_4c4c


title: nasal_epithelial_cell, edae_4105


title: CTC17M

city: Bangkok

first: Thanawat

last: Suwatthanarak

address: 2 Wanglang Road, Bangkok-Noi

country: Thailand

institute: Mahidol University

description: FFPE spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline.
Sequences were alinged to mm10 geonome using the 10x Genomics Space Ranger's default settings.
Gene expression level was quantified using the 10x Genomics Space Ranger's default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene exprssion count data in Matrix Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.cvs.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Colorectal cancer

extract_protocol:
FFPE tissues was sectioned with cryostat (5 micrometer).
Libraries were prepared using the 10x Genomics Visium Spatial Gene Expression Slides and the reagent kit according to the manufacturer's instruction.

value: Colorectal cancer

tag: tissue type

value: metastasis tissue

value: Circulating tumor cells

tag: patient id


title: CTC17P

description: FFPE spatial transcriptome sequencing

value: primary tissue


title: nasal_epithelial_cell, 30ec_42e2


title: nasal_epithelial_cell, 81c3_49b6


title: CTC21M

description: FFPE spatial transcriptome sequencing


title: CTC21P

description: FFPE spatial transcriptome sequencing


title: PBMCs, B3

city: Shenzhen

first: Ying

last: Wang

address: xinan

department: Shenzhen hospital

country: China

institute: southern mecical university

data_processing:
1) Removal of the 3' end of the junction using Cutadapt, with the removed portion having at least a 10 bp Overlap (AGATCGGAAG) to the known junction, allowing for 20% base mismatches;2) Remove Reads with an average mass fraction below Q20
Filtered Reads were aligned to the reference genome using the upgraded version of TopHat2, HISAT2(http://ccb.jhu.edu/software/hisat2/index.shtml) software. HISAT2 uses an improved BWT algorithm that is faster and has a lower resource footprint. HISAT2 uses default parameters for non-strand-specific libraries, and requires the library type to be specified for strand-specific libraries (i.e., use --rna-strandness RF for first, --rna-strandness FR for second).
We analysed expression saturation using RSeQC, i.e.: sequencing results were analysed at 5%, 10%, 15%.... . 100%.The expression of all genes was calculated separately for different sampling ratios (i.e., 20 times for each gene), and then compared with the actual expression to get the relative error.
Assembly: hg38
Supplementary files format and content: expression.txt (read count, fpkm)

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chainreaction (PCR) amplified.

tag: treatment

value: control


title: nasal_epithelial_cell, 6760_4c59


title: nasal_epithelial_cell, 672e_4cc4

value: female


title: PBMCs, F3

value: FEV


title: PBMCs, F1


title: PBMCs, F2


title: nasal_epithelial_cell, b123_4bae

value: male


title: nasal_epithelial_cell, 5890_4cdc


title: PBMCs, B2


title: PBMCs, B1


title: HL-60 wild type, replicate 2

city: Dijon

first: Laurent

last: DELVA

address: 7 boulevard Jeanne d’Arc

department: Inserm U1231 (CTM)

country: France

institute: Université de Bourgogne

data_processing:
Quality control of raw reads was done with FastQC_0.11.8
Reads were mapped to GRCh38_primary_assembly with STAR-2.7.6a
Read counts was done as same time as mapping using the «GeneCounts» mode of STAR-2.7.6a, on the ensembl assembly «Homo_sapiens.GRCh38.104.chr.gtf» (parameters – twopassmod: basic)
Normalization and differential expression were performed with the R package DESeq2
Assembly: GRCh38_primary_assembly
Supplementary files format and content: Tab-delimited text file includes raw count for each sample (STAR2 count)
Supplementary files format and content: Tab-delimited text file includes DESeq2 analysis results + normalized counts

growth_protocol: The human AML cell line HL-60 and subclones were grown in RPMI 1640 with L-Glutamine supplemented with 10% FBS and 1% of antibiotics

extract_protocol:
1 million cells were harvested for each sample and total RNA was extracted in TRIzol™ reagent and eluted in 15 µl of RNAse-free water. RNA-seq was performed by GENEWIZ (Azenta Life Sciences).
Made by GENEWIZ (Azenta Life Sciences)

tag: cell line

value: Acute Myeloid Leukemia

tag: genotype

value: WT


title: HL-60 wild type, replicate 3


title: nasal_epithelial_cell, 2843_4d06


title: nasal_epithelial_cell, 306b_4239


title: HL-60 wild type, replicate 1


title: nasal_epithelial_cell, 4358_48f6


title: HL-60 PRMT2 KO, AA14 clone, replicate 3

value: PRMT2 knockout


title: nasal_epithelial_cell, 7dbf_4a38


title: nasal_epithelial_cell, 168a_46da


title: HL-60 PRMT2 KO, AA14 clone, replicate 2


title: nasal_epithelial_cell, 7721_4c00


title: HL-60 PRMT2 KO, AA14 clone, replicate 1


title: nasal_epithelial_cell, c756_455d


title: nasal_epithelial_cell, 9686_44ed


title: nasal_epithelial_cell, e19e_423a


title: HL-60 PRMT2 KO, AA13 clone, replicate 3


title: nasal_epithelial_cell, 4da3_4dc3


title: HL-60 PRMT2 KO, AA13 clone, replicate 1


title: PIM231

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

data_processing:
The gene expression data was sequenced in six separate batches and preprocessed using the same pipeline.
We processed the data using the BETSY system, which aligned the reads to the hg19 genome with STAR estimated the transcript abundance as transcripts per million (TPM) with RSEM.
We applied ComBat to log_2 TPM values for batch effect normalization.
Assembly: hg19
Supplementary files format and content: expression.txt is a tab-delimited text file that contains the batch normalized gene expression values.

source_name: Breast

growth_protocol: The fourth mammary fat pads of 4-to-8-week-old female NOD/SCID mice were implanted with 500,000 PDX tumor cells suspended in 30 µL of a 50:50 mixture of DMEM/F12 media and Matrigel. Cells in Matrigel were maintained on ice until engraftment.

extract_protocol:
The RNA was extracted using PicoPure RNA isolation kit and RNA concentration was quantified by Nanodrop.
Whole transcriptome RNA-seq libraries were prepared using RNA HyperPrep kit with RiboErase following the manufacturer's instructions. 100bp paired-end sequencing was performed on NovaSeq 6000 using S4 Reagent Kit with 48 libraries pooled per lane.

treatment_protocol: Patients were treated with neoadjuvant chemotherapy.  Tumors were extracted and engrafted into xenograft mouse models before (Pre), during (Mid), and after (Post) treatment.

value: Breast, xenograft of patient-derived tumor tissue

tag: tumor type

value: Triple Negative Breast Cancer

tag: tnbc subtype

value: M

tag: time point

value: mid


title: nasal_epithelial_cell, fed0_47e3


title: PIM300

value: pre


title: nasal_epithelial_cell, 3a0b_4661


title: PIM190


title: nasal_epithelial_cell, 527c_4f5b


title: PIM328

value: post


title: nasal_epithelial_cell, f6c8_4448


title: PIM077


title: nasal_epithelial_cell, 8fcf_4f7a


title: nasal_epithelial_cell, 9c97_4ba2


title: PIM172

value: UNS


title: PIM137


title: PIM038


title: nasal_epithelial_cell, b30d_4fdf


title: nasal_epithelial_cell, 6d32_4b2f


title: PIM163


title: nasal_epithelial_cell, 056a_46b7


title: nasal_epithelial_cell, f1c8_44f8


title: nasal_epithelial_cell, 6c2a_4ed9


title: PIM051


title: PIM040

value: LAR


title: nasal_epithelial_cell, 9ad1_4abc

value: hispanic


title: HL-60 PRMT2 KO, AA13 clone, replicate 2


title: nasal_epithelial_cell, 07d9_4d0f


title: PIM164


title: PIM254


title: nasal_epithelial_cell, 652d_42ea


title: PIM053


title: PIM091


title: nasal_epithelial_cell, 42c4_4b88


title: PIM024


title: PIM056


title: PIM014


title: PIM284


title: PIM321


title: PIM025


title: nasal_epithelial_cell, 1006_4774


title: nasal_epithelial_cell, 248d_4253


title: nasal_epithelial_cell, 9295_4689


title: nasal_epithelial_cell, 15d2_461c


title: PIM262


title: nasal_epithelial_cell, 8aab_4c0b


title: nasal_epithelial_cell, e8bf_41af


title: nasal_epithelial_cell, 71ca_4a54


title: PIM010


title: PIM046


title: nasal_epithelial_cell, 7be3_4ec6

value: multiple


title: PIM068


title: nasal_epithelial_cell, de77_4175


title: nasal_epithelial_cell, b9f0_47ed


title: nasal_epithelial_cell, e102_440b


title: PIM269


title: nasal_epithelial_cell, 6508_4851


title: PIM242


title: nasal_epithelial_cell, b1f9_4523


title: PIM404


title: PIM407


title: PIM388


title: nasal_epithelial_cell, 66a5_4755


title: PIM387


title: nasal_epithelial_cell, 8aae_47c9


title: nasal_epithelial_cell, eea3_4562


title: PIM393


title: PIM402


title: PIM311


title: nasal_epithelial_cell, f89e_4833


title: nasal_epithelial_cell, 9100_42ec


title: nasal_epithelial_cell, 5b52_438b


title: nasal_epithelial_cell, 9dc0_4ad1


title: nasal_epithelial_cell, 03fa_4cf3


title: nasal_epithelial_cell, 4b43_4c89


title: BT88_noGF

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

institute: inserm inm u1191

description: 10X Genomics

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and the Real-Time Analysis component (Illumina). Demultiplexing was performed using the 10x Genomics software Cellranger mkfastq.gz (v7.1.0), a wrapper of Illumina's bcl2fastq.gz (v2.20). The quality of the raw data was assessed using fastq.gzC (v0.11.9) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). fastq.gzScreen (v0.15.1) was used to identify potential contamination. Alignment, gene expression quantification and statistical analysis were performed using Cell Ranger count with the human's transcriptome (GRCh38). In order to discard ambient RNA falsely identified as cells, Cell Ranger count was run a second time with the option --force-cells to force the number of cells to detect. Cell Ranger aggr was used to combine each sample results into one single analysis.
Assembly: GRCh38
Supplementary files format and content: 10X CellRanger output Market Exchange Format (MEX) files (barcodes, features, and matrix files).

source_name: high  grade brain tumor

growth_protocol: Glioma cell lines were grown in a defined media as neurospheres in the growth factor (GF) conditions and then plated on PDL-Laminin-coated coverslips without growth factor (noGF) for differentiation

extract_protocol:
Cells were dissociated from 2D cultures or 3D neurosphere cultures into single cell suspensions.
Cell suspensions were loaded on a Chromium controller (10x Genomics, Pleasanton, CA) to generate single-cell Gel Beads-in-Emulsion (GEMs). The single-cell RNA-Seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits V3.1 (Dual Index, P/N 1000268, 10x Genomics). Briefly, reverse transcription was performed at 53°C for 45 min followed by incubation at 85°C for 5 min. GEMs were then broken and the single-stranded cDNAs were cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific; P/N 37002D). The cDNAs were PCR amplified, cleaned up with SPRIselect beads (SPRI P/N B23318), fragmented, end-repaired, A-tailed, and size-selected with SPRIselect beads. Indexed adapters were ligated and cleaned up with SPRIselect beads. The resulting DNA fragments were PCR amplified and size-selected with SPRIselect beads. The size distribution of the resulting libraries was monitored using a Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) and the libraries were quantified using the KAPA Library quantification kit (Roche, Basel, Switzerland). The libraries were denatured with NaOH, neutralized with Tris-HCl, and diluted to 150 pM. Clustering and sequencing were performed on a NovaSeq 6000 (Illumina, San Diego, CA, USA) using the paired- end 28-90 nt protocol on one lane of an SP flow cell and on one lane of an S4 flow cell.

value: high  grade brain tumor

value: oligodendroglioma

tag: tumor grade

value: grade 3

value: neural progenitor like cells

value: IDH1 wt

value: without growth factor


title: BT88_GF

description: 10X Genomics

value: with growth factor


title: BT54_noGF

description: 10X Genomics

value: IDH1 mutant


title: nasal_epithelial_cell, 673c_46f6

tag: Sex

value: female


title: nasal_epithelial_cell, a2e2_4726

value: male

tag: proportionpositiveskinpricktests


title: nasal_epithelial_cell, a595_4a45

tag: plate


title: nasal_epithelial_cell, 6e37_46d2

tag: ageindays


title: BT237_GF

description: 10X Genomics


title: nasal_epithelial_cell, d4a7_4dea

tag: cohort (the year of sample recruitment)


title: BT138_noGF

description: 10X Genomics


title: nasal_epithelial_cell, 76af_40bb

tag: array


title: nasal_epithelial_cell, 127d_423b


title: nasal_epithelial_cell, d85e_40fb


title: nasal_epithelial_cell, 9c5a_4a13


title: nasal_epithelial_cell, d4ac_4c32


title: LGG336_GF

description: 10X Genomics

source_name: low grade brain tumor

tag: tissue

value: low grade brain tumor

value: astrocytoma

value: grade 2


title: LGG349_GF

description: 10X Genomics

source_name: high grade brain tumor

value: high grade brain tumor

value: grade 4

tag: cell type


title: LGG349_noGF

description: 10X Genomics


title: BT237_noGF

description: 10X Genomics


title: nasal_epithelial_cell, ca4e_44db


title: LGG85_noGF

description: 10X Genomics


title: nasal_epithelial_cell, f00a_4c60


title: LGG85_GF

description: 10X Genomics


title: nasal_epithelial_cell, 63a8_47d2


title: LB

city: Xi‘an

first: sy

last: w

address: Changle West Road 145

institute: fmmu

description: 10x Genomics

data_processing:
Unsupervised clustering and differential gene analyses were performed using the Seurat package. Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters.
Assembly: h38
Supplementary files format and content: Tap-seperated values and matrix files

source_name: oral mucosa

extract_protocol:
Fresh isolated human oral mucosal tissue specimens were rinsed with HBSS, cut into small pieces, and filtered twice through 40um filters for single-cell analysis.
Guided by 10X manufacturer’s protocols, single cell cDNA library was prepared and sequenced. Briefly, single cell suspension was loaded on a Chromium controller to obtain single cell GEMS (Gel Beads-In-Emulsions) for the reaction. The library was prepared with Chromium Next GEM single cell 3’ kit V2 (10X Genomics) and sequenced on Illumina Novaseq 6000.

value: oral mucosa

tag: subject status

value: control


title: 6-9-1nm

description: 10x Genomics

value: OSF (Oral Submucous Fibrosis) patient


title: nasal_epithelial_cell, 1c74_4d74


title: HepG2 Mtb INFECTED (48 hour post infection), 4

city: New Delhi

first: Debasisa

last: Mohanty

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Imunology

data_processing:
The fastp tool was used to remove low qulaity reads and trimming the adapters.
Processed reads were mapped to reference genome (reference: mm9) using hisat2 tool.
Assembly and Quantification were done using stringtie. Further, DESeq2 used for the differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: csv

growth_protocol: HepG2 cells were grown in DMEM-high glucose supplimented with 10% FBS and antibiotics in a humidified atmosphere at 37degree Celsius

extract_protocol:
Total RNA was isolated using Macherey-Nagel (MN) Nucleospin RNA isolation kit
Library was prepared using Illumina stranded total RNA prep kid as per manufacturer protocol

treatment_protocol: HepG2 cells were infected with Mtb-H37Rv-mCherry at multipliction of infection 10 and sorted for mCherry positive cells at 0 hours (5 hours post infection) and 48 hours post infection.

value: Heptocytes

value: Mtb-H37Rv-mCHerry, MOI 10


title: BT138_GF

description: 10X Genomics

value: high  grade brain tumor

value: oligodendroglioma

value: grade 3

value: neural progenitor like cells


title: nasal_epithelial_cell, ac57_41f3

value: hispanic


title: HepG2 Mtb INFECTED (48 hour post infection), 2


title: HepG2 Mtb INFECTED (48 hour post infection), 3


title: nasal_epithelial_cell, 099d_4201

value: female


title: nasal_epithelial_cell, 5abe_4ffe


title: nasal_epithelial_cell, d9ba_4278

value: male


title: HepG2 Mtb INFECTED (48 hour post infection), 1


title: LGG275_GF

description: 10X Genomics

value: low grade brain tumor

value: IDH1 mutant

value: with growth factor


title: LGG336_noGF

description: 10X Genomics

value: astrocytoma

value: grade 2

value: without growth factor


title: nasal_epithelial_cell, b8dc_44e7


title: HepG2 Mtb UNINFECTED, 48 hours,  4

value: No infection


title: nasal_epithelial_cell, ef93_4fd7


title: nasal_epithelial_cell, d9b2_451f


title: nasal_epithelial_cell, 4647_463e


title: LGG275_noGF

description: 10X Genomics


title: HepG2 Mtb UNINFECTED, 48 hours , 2


title: HepG2 Mtb UNINFECTED, 48 hours ,1


title: HepG2 Mtb INFECTED (0 hour post infection)(5 hour post incubation), 4


title: BT54_GF

description: 10X Genomics


title: nasal_epithelial_cell, 9c1c_4567


title: nasal_epithelial_cell, 2e0d_476a


title: nasal_epithelial_cell, eb64_4d92


title: HepG2 Mtb INFECTED (0 hour post infection)(5 hour post incubation), 3


title: HepG2 Mtb INFECTED (0 hour post infection)(5 hour post incubation), 2


title: HepG2 Mtb INFECTED (0 hour post infection)(5 hour post incubation) ,1


title: nasal_epithelial_cell, c14e_47f0


title: HepG2 Mtb UNINFECTED, 0 hour, 4


title: HepG2 Mtb UNINFECTED, 0 hour, 3


title: nasal_epithelial_cell, 8c8a_4538


title: nasal_epithelial_cell, 2490_4ae7


title: nasal_epithelial_cell, 362e_48df


title: HepG2 Mtb UNINFECTED, 0 hour, 1


title: nasal_epithelial_cell, 2693_44c9


title: nasal_epithelial_cell, b657_4d43


title: nasal_epithelial_cell, 0483_42ba


title: HepG2 Mtb UNINFECTED, 0 hour, 2


title: Pt_#8, replicate B, TCR-seq

city: Philadelphia

first: Renzo

last: Perales-Linares

state: PA

address: 3675 Market Street, Suite 200

department: Research and Development

institute: Geneos Therapeutics

description: 10x Genomics

data_processing:
*library strategy: TCR-seq
Cell Ranger v6.0.0 was used to demultiplex FASTQ reads, perform sequence alignment to the GRCh38 transcriptome, and extract unique molecular identifier (UMI) barcodes.
Assembly: GRCh38
Supplementary files format and content: Gene expression data are in tab-separated values files and matrix files. T cell receptor repertoire files are in comma-separated values files.

source_name: peripheral blood

extract_protocol:
T cells were isolated and enriched from week 12 post-treatment PBMC using the human Pan T Cell Isolation Kit (Miltenyi Biotec, MD) following the manufacturer’s instructions.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single-Cell 5’ Reagent kit v2 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run. Sequencing for each library targeted 20,000 mean reads per cell.

value: peripheral blood

value: T cell

value: 12-week post-vaccination

value: vaccine + pembrolizumab


title: Pt_#8, replicate A, TCR-seq

description: 10x Genomics


title: nasal_epithelial_cell, 741d_4760


title: Pt_#8, replicate B, scRNA

description: 10x Genomics

data_processing:
Cell Ranger v6.0.0 was used to demultiplex FASTQ reads, perform sequence alignment to the GRCh38 transcriptome, and extract unique molecular identifier (UMI) barcodes.
Assembly: GRCh38
Supplementary files format and content: Gene expression data are in tab-separated values files and matrix files. T cell receptor repertoire files are in comma-separated values files.


title: Pt_#8, replicate A, scRNA

description: 10x Genomics


title: Pt_#7, replicate A, TCR-seq

description: 10x Genomics


title: nasal_epithelial_cell, 629c_4c5a


title: nasal_epithelial_cell, d528_46ce


title: HepG2 Mtb UNINFECTED, 48 hours,  3

value: Heptocytes


title: Pt_#6, replicate A, TCR-seq

description: 10x Genomics


title: nasal_epithelial_cell, d23b_44ce


title: nasal_epithelial_cell, 0ae6_4230


title: Pt_#7, replicate A, scRNA

description: 10x Genomics


title: Pt_#6, replicate A, scRNA

description: 10x Genomics


title: nasal_epithelial_cell, 41b8_44af


title: human primary decidual immune cells, scRNA-seq

city: Shanghai

first: Zhidan

last: Li

address: Ruijin er road 207

institute: NIPD

description:
10x Genomics
R22002572-OES213959100-OES213959100-01_combined

data_processing:
The raw data generated from high-throughput sequencing are in fastq format, and in order to ensure the quality of sequencing, FastQC software was used to assess the quality of the raw downstream data.CellRanger, the official software of 10x genomics, was used to perform data quality statistics on the raw data and comparison with the reference genome. The software quantified the high-throughput single-cell transcriptome by identifying the Barcode sequence markers that distinguish the cells in the sequences and UMI markers that distinguish the mRNA molecules in each cell, so that we could obtain the high-quality statistical information such as the number of cells, the median value of genes, the saturation level of sequencing and other quality control information. saturation and other quality control statistics.
The Seurat software package was used to further quality control and process the data based on the initial Cellranger QC results.Theoretically, the number of genes expressed in most cells, the number of UMIs and the mitochondrial gene expression will be concentrated in a certain region. Based on this feature, we first filtered the off-domain cells by fitting a generalized linear model, and then filtered the mitochondrial gene expression according to the nUMI, nGene Based on this characteristic, we firstly filtered the outlying cells by fitting the generalized linear model, and then filtered out the low-quality cells such as two-cells, multi-cells or dead cells according to the distribution of nUMI, nGene and percent.
Based on the initial QC of Cell Ranger, the experimental data were further QC'd to exclude multi-cell, two-cell, or non-cell-bound data. The quality control criteria in this project were to retain cells with gene counts and UMI counts within the median ± 2-fold absolute median difference and with less than 5% mitochondrial UMIs as high-quality cells, and then perform double-cell removal for downstream analysis using DoubletFinder software.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz (INF is barcode-1 and NOR is barcode-2;  see clustering_results.csv), features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: human primary decidual immune cell

extract_protocol:
Single cells were suspended in calcium and magneslum-free PBS containing 0.04% weight/voiume BSA.
RNA libraries were prepared withChromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.The 10x Genomics platform utilizes microfluidic technology to wrap the bead and cell with Cell Barcode in a droplet, collect the droplet with the cell, and then lysed the cell in the droplet, so that the mRNA in the cell is linked to the Cell Barcode on the bead to form Single Cell GEMs, and then reverse transcribe the cDNA in the droplet to construct cDNA libraries. Reverse transcription is performed in the droplet to construct a cDNA library, and the sample index on the library sequence distinguishes the sample source of the target sequence.

value: Primary cells, not cell lines

value: human decidual immune cells

tag: infection

value: uninfected


title: nasal_epithelial_cell, 72b7_4daf

value: female

value: multiple


title: T. gondii-infected human primary decidual immune cells, scRNA-seq

description:
10x Genomics
R22002561-OES213958100-OES213958100-01_combined

value: T. gondii


title: nasal_epithelial_cell, ac6b_44df

value: male


title: nasal_epithelial_cell, bc2a_4808

value: hispanic


title: USP43 KO normoxia biol rep 3

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with TrimGalore
Transcript quantification was performed using Salmon
Differential transcript analysis was performed with DESeq2
Assembly: Gencode Human Release 44 (GRCh38.p14)
Supplementary files format and content: Salmon quant files that contain TPM values for each transcript

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM and supplemented with 10% FCS

extract_protocol:
Total RNA was extracted from HeLa cells using the RNeasy Plus minikit.
RNA libraries for RNA-Seq were prepared by GeneWiz (NEBNext Ultra II RNA Library Prep Kit)

treatment_protocol: Hypoxic cell culture was performed in a Whitley H35 Hypoxystation at 37 °C, 5% CO2, 1 % O2and 94% N2.

value: HeLa

value: USP43 KO

tag: treatment

value: normoxia


title: nasal_epithelial_cell, 8bee_4d2d


title: nasal_epithelial_cell, 6774_4eef


title: USP43 KO normoxia biol rep 2

tag: cell line


title: nasal_epithelial_cell, a683_4c9b


title: nasal_epithelial_cell, e89b_4175


title: USP43 KO hypoxia biol rep 2

tag: genotype

value: hypoxia


title: nasal_epithelial_cell, 953a_4bcb


title: HIF1B KO normoxia biol rep 3

value: HIF1B KO


title: USP43 KO normoxia biol rep 1


title: nasal_epithelial_cell, 275f_49fc


title: nasal_epithelial_cell, 4d63_4379


title: USP43 KO hypoxia biol rep 3


title: USP43 KO hypoxia biol rep 1


title: nasal_epithelial_cell, d7ac_4405


title: HIF1B KO normoxia biol rep 1


title: nasal_epithelial_cell, c9a1_4815


title: nasal_epithelial_cell, 46ad_4fea


title: KO_RAPA_AAV_Liver_R3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

data_processing:
QC: FastQC ( v0.11.9 )
Filters: cutadapt ( 1.18 ), PRINSEQ-lite ( 0.20.4 )
Mapping & QC: STAR ( 2.7.6a ), samtools ( 0.1.18 )
Counting: HTSeq-count ( 0.12.4 )
Assembly: EnsEMBL Mouse GRCm38.99
Supplementary files format and content: Raw counts of each sample (XLSX, NGS79_readscounts_raw_55471genes)

organism: Mus musculus

source_name: Liver

growth_protocol: Immediately after euthanasia, mouse triceps and a piece of liver were snap-frozen in isopentane (-160°C) previously chilled in liquid nitrogen.

extract_protocol:
RNA was isolated using RNeasy Plus Mini extraction kit (Qiagen,Germany) according to the manufacturer’s instructions. DNase I digestion (Invitrogen, USA) was performed to degrade DNA in the sample.  Quantification and quality control of RNA samples were determined using Agilent RNA ScreenTape System (Agilent, USA)  following manufacturer’s instructions.
For each sample, 100 ng of total RNA was used to perform the QuantSeq 3' mRNA-Seq Library Prep FWD for Illumina (Lexogene, Vienna, Austria) resulting in NGS libraries which originate from the 3' end of polyadenylated RNA. Briefly, library generation was started by oligo(dT) priming with primers. After first strand synthesis, the RNA was removed before the second strand synthesis was initiated by random primers. Libraries were PCR amplified and barcoded in 17 cycles and were quantified using Agilent High Sensitivity DNA kit (Agilent). 2nM of pooled libraries were denatured and 1.8pM was used for cluster generation before single-end sequencing on an Illumina Nextseq550 (Illumina, US).

treatment_protocol: Six-month-old Agl+/+ and Agl-/- mice were injected daily intraperitoneally with 1.5 mg/kg rapamycin or vehicle. After a month, half of the Agl-/- mice treated with vehicle were injected intravenously with 2 x 1012 vg total of AAV9-LiMP-GDE overlapping vector (n=4), or PBS (n=4); and half of the Agl-/- mice treated with rapamycin were injected intravenously with 2 x 1012 vg total of AAV9-LiMP-GDE overlapping vector (n=4), or PBS (n=3). Rapamycin daily injections were pursued for 15 additional days in these two last groups as well as in the Agl+/+, rapamycin group. Agl+/+ mice treated with vehicle (n=3) have been used as controls.

value: Liver

tag: replicate

tag: breading

value: Agl KO


title: KO_RAPA_AAV_Liver_R4


title: HIF1B KO hypoxia biol rep 1


title: HIF1B KO normoxia biol rep 2


title: HIF1B KO hypoxia biol rep 3


title: nasal_epithelial_cell, d675_4be0


title: HIF1B KO hypoxia biol rep 2


title: Control normoxia biol rep 3

value: Control


title: Control normoxia biol rep 2


title: nasal_epithelial_cell, 1fed_48e1


title: Control normoxia biol rep 1


title: Control hypoxia biol rep 3


title: Control hypoxia biol rep 2


title: KO_RAPA_AAV_Liver_R1


title: nasal_epithelial_cell, 6da6_4c3b


title: Control hypoxia biol rep 1


title: KO_RAPA_AAV_Liver_R2


title: KO_CTL_AAV_Liver_R3


title: nasal_epithelial_cell, e369_4090


title: TNBC tissue, replicate 3 [Spatial Transcriptome]

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

description:
YZL1
10x Spatial Transcriptome sequencing

data_processing:
*library strategy: Spatial transcriptomics
Each sequenced spatial transcriptomics library was processed and aligned to hg38 reference genome using Space Ranger software (version 2.0.0) from 10x Genomics, with UMI counts summarized for each spot. To distinguish tissue overlaying spots from the background, tissue overlaying spots were detected according to the images. And only barcodes associated with these tissue overlaying spots were retained, with the filtered UMI count matrices generated. We also manually excluded spots not covered by tissue but not detected by Space Ranger and further filter the UMI count matrices.
After imported into R, the filtered UMI count matrix was analyzed using the R package Seurat (version 4.1.0). Regularized negative binomial regression (SCTransform) was used to normalize UMI count matrices. Four（based on sample number） matrices from the fourbased on sample number） slices were merged to analyze them together. 3,000 highly variable genes were identified in each matrix, and the union set of them was set as highly variable genes for the merged data and used in principal component analysis to reduce dimensionality. We determined to use the first 30 principal components in clustering analysis according to the elbow plot. Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction was performed with the first 30 principal components as input to visualize spots.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: breast tissue

extract_protocol:
OCT blocks were sectioned at 10μm in thickness, 6.5mm X 6.5mm in size,attached to the Visium slides, then stained with hematoxylin and eosin following 10x Genomics Visium fresh frozen tissue processing protocol.
H&E Images were taken by a fluorescence and tile scanning microscope (Olympus Fluoview 1000) then the slides underwent tissue removal and library generation per 10x Genomics demonstrated protocol.

value: breast tissue

tag: tissue type

value: triple negative breast cancer


title: nasal_epithelial_cell, 13ec_4c61


title: KO_CTL_AAV_Liver_R2


title: TNBC tissue, replicate 1 [Spatial Transcriptome]

description:
SXR1
10x Spatial Transcriptome sequencing


title: nasal_epithelial_cell, 63a4_440c


title: TNBC tissue, replicate 2 [Spatial Transcriptome]

description:
SXR2
10x Spatial Transcriptome sequencing


title: TNBC tissue, replicate 2

description:
LC2103443
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
We used the Seurat R package (v4.1.3) to perform unsupervised clustering of the single cells using the reads count matrix as input. First, the read counts for each cell were divided by the total counts for that cell and multiplied by the scale factor (10,000), and then natural-log transformed. We performed principal component analysis (PCA) on the normalized expression matrix using highly variable genes identified by ‘‘SCTransform’’ function
harmony R package “RunHarmony“ was used to remove the batch effect between samples. Following the results of Harmony, the appropriate principal components (Harmonys) were selected for clustering with the specific resolution parameters. Finally, to detect cluster-specific expressed genes, the clusters were compared pairwise using the Seurat ‘‘FindAllMarkers’’ function to test genes with > 0.25-fold difference (log-scale) on average between the two groups of cells.
For the clustering of all cells, the top 25 Harmonys were selected with a resolution parameter equal to 0.6. For the clustering of T lymphocytes,the top 20 PCs were selected with a resolution parameter equal to 1.
Marker genes for each cluster were identified with the Wilcoxon rank-sum test with default parameters via the FindAllMarkers function in Seurat。differential expression analysis was carried out using ‘‘FindMarkers’’ function, implemented in the Seurat package, with log-scaled fold change >=0.25 and P value <= 0.05 (Wilcoxon Rank Sum test)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
Fresh tumor and adjacent normal tissue samples were surgically removed from patients and immersed in a complete medium containing 90% Dulbecco’s modified eagle medium (DMEM; Cat# 11054001, GIBCO) and 10% fetal bovine serum (FBS; Cat# 16140071, GIBCO), and transported to the lab in a refrigerated container. Suitable small tissue blocks (no necrotic foci / no hemorrhagic foci /less fibrous connective tissue) were cut into pieces (diameter 1-3 mm). The pieces were transferred to the gentle MACS C Tubes (Cat# 130-096-334, Miltenyi Biotec), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Cat# 130-095-929, MiltenyiBiotec). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Cat# 130-093-235, MiltenyiBiotec) following these steps: milled; incubated at 37C for 30 min on a shaker; milled; incubated at 37C for 30 min; milled; filtered through a 70 mm filter, plus 2% FBS. Finally, the single-cell suspension was centrifugated at 400 g for 7 mins, resuspended in CELLSAVING (Cat# C40050, NCM biotech), cryopreserved in Cryotubes (Cat# 430488, Corning) and then stored at -80℃.
This process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not conThis process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not contain cells, and most of the remaining GEM contained one cell


title: TNBC tissue, replicate 1

description:
LC2101086
10x Genomics


title: nasal_epithelial_cell, 56bc_4099


title: Cancer2_Neu_post

city: Bethesda

first: Gustaf

last: Wigerblad

state: MD

address: 10 Center Dr

department: NIAMS

institute: National Institutes of Health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v 7.1.0)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood was collected in heparin tubes and neutrophils were extracted using negative selection kit from StemCell
Library construction was performed in accordance with 10X Genomics protocol (Chromium Next GEM Single Cell 3' Gene expression (GEX) library protocol, v3.1).
Single-cell RNA-sequencing (3'-v3.1)

value: Blood

value: Neutrophil

value: BTK-inh


title: KO_CTL_AAV_Liver_R1


title: Cancer1_Neu_post

description: 10x Genomics


title: KO_RAPA_Liver_R3

value: RAPA


title: Cancer3_Neu_post

description: 10x Genomics


title: KO_RAPA_Liver_R2


title: Cancer2_Neu_pre

description: 10x Genomics

value: No treatment


title: nasal_epithelial_cell, 7df0_47ea

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5%) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using ENmix. Please see https://github.com/hansenlab/IlluminaHumanMethylationAllergymanifest/tree/4a00cd62600a662f9a5f1cd32b5aeecee87225a8 for annotation and manifest packages.
MatrixProcessed.txt:  ENmix normalized Beta values
SignalIntensities.txt:  Unmethylated and methylated signal intensities after background normalization.

value: female


title: KO_CTL_AAV_Liver_R4


title: MZ1GSK rep3

city: Shinagawa-ku

first: Fumiaki

last: Ohtake

state: Tokyo

country: Japan

institute: Hoshi University

data_processing:
Trimmed reads are mapped to reference genome with HISAT2.
After the read mapping, Stringtie was used for transcript assembly.
Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
Assembly: GRCh38, NCBI_109.20200522
Supplementary files format and content: Excel file containing FPKM and TPM for each sample

growth_protocol: Human HCT116 cells were obtained from ATCC and maintained at 37°C with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) high-glucose medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich), penicillin–streptomycin (100 units/mL, GIBCO #15140148), sodium pyruvate (1 mM, GIBCO #11360070), and MEM nonessential amino acids (1×, GIBCO #11140050).

extract_protocol:
Total RNA was isolated using RNeasy kit (QIAGEN)
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA LT Sample Prep Kit following manufacturer's protocol.

treatment_protocol: HCT116 cells were treated with either PDD, GSK, or MZ1 for 24 h, and total RNA was isolated.

tag: disease

value: Colon cancer

value: WT

value: MZ1 and GSK


title: nasal_epithelial_cell, 7134_4ab4

extract_protocol: Flocked nasal swabs were obtained at age 5-7 years and samples were stored at -80, then extracted using AllPrep DNA/RNA kit (Qiagen) following the manufacturer's protocol.

tag: Sex


title: KO_RAPA_Liver_R1


title: MZ1GSK rep2


title: KO_CTL_Liver_R4

value: CTL


title: nasal_epithelial_cell, fd73_44f6

value: male

tag: proportionpositiveskinpricktests


title: MZ1PDD rep3

value: MZ1 and PDD


title: MZ1PDD rep1


title: MZ1PDD rep2


title: KO_CTL_Liver_R3

value: Liver


title: MZ1 rep3


title: nasal_epithelial_cell, 701b_47f2

tag: plate


title: nasal_epithelial_cell, a856_4e3f

tag: ageindays

value: multiple


title: Cancer3_Neu_pre

description: 10x Genomics


title: nasal_epithelial_cell, 4be2_42fb

tag: cohort (the year of sample recruitment)


title: KO_CTL_Liver_R1

value: Agl KO


title: MZ1 rep2


title: GSK rep3

value: GSK


title: WT_CTL_Liver_R3


title: Cancer1_Neu_pre

description: 10x Genomics


title: nasal_epithelial_cell, 0f4b_42e4

tag: array


title: GSK rep2


title: GSK rep1


title: WT_CTL_Liver_R2

tag: tissue


title: PDD rep3

value: PDD


title: nasal_epithelial_cell, c6cf_4108


title: PDD rep2


title: MZ1GSK rep1


title: PDD rep1


title: nasal_epithelial_cell, a75c_453d


title: KO_CTL_Liver_R2


title: nasal_epithelial_cell, fbdd_4081


title: Control rep2

value: vehicle


title: KO_RAPA_AAV_Triceps_R4

source_name: Triceps

value: Triceps


title: nasal_epithelial_cell, f6a0_49e7


title: KO_RAPA_AAV_Triceps_R3


title: nasal_epithelial_cell, ded1_433f


title: nasal_epithelial_cell, 382d_48c0


title: scTCR-seq_P605

city: Beijing

first: Yuxuan

last: Sun

address: Yiheyuan Road

institute: Peking University

description:
10X Genomics
Real/RWC

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 6.1.2), employing GRCh38 as the reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 6.1.2) with the manufacturer-supplied human VDJ reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: lung

extract_protocol:
Fresh tumor tissues were cut into pieces of approximately 1mm3 in the RPMI-1640 medium (Gibco, 11875093) with 10% fetal bovine serum (FBS; Gibco, 10099141), and enzymatically digested with Tumor Dissociation Kit (Miltenyi, 130-095-929) for 60 minutes on a rotor at 37 °C. Dissociated cells were subsequently passed through a 100μm MACS SmartStrainers (Miltenyi, 130-110-917) and centrifuged at 300g for 8 minutes. After removing supernatant, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ, 90309-100) and incubated on ice for 5 minutes to lyse red blood cells. After washing with PBS (Gibco, 10010023), cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% FBS). Single-cell suspensions were then stained with 7-AAD Viability Staining Solution (Invitrogen, 00-6993-50) and an antibody against CD235a (BioLegend, 349114) for FACS sorting on a BD Aria III instrument. Non-erythrocytic living cells were enriched by gating 7AAD−CD235a− cells. The concentration of single-cell suspensions was then adjusted to 700~1,200 cells μl–1 and single-cell suspensions with viable cell rate greater than 80% were used for single cell sequencing.
In total, ~18,000 cells for each sample were used for 10X Chromium Single cell 5′ and human TCR library construction (10X Genomics), according to the manufacturer’s instructions. All subsequent steps were performed following the standard manufacturer protocols. Purified libraries were subsequently sequenced using an Illumina NovaSeq 6000 sequencer with 150-base pair (bp) paired-end reads.

value: lung


title: MZ1 rep1


title: scTCR-seq_P609

description:
10X Genomics
Real/RWC


title: scTCR-seq_P579

description:
10X Genomics
Real/RWC


title: scTCR-seq_P592

description:
10X Genomics
Real/RWC


title: scTCR-seq_P603

description:
10X Genomics
Real/RWC


title: KO_RAPA_AAV_Triceps_R1


title: nasal_epithelial_cell, 2eb7_40ac

city: Chicago

first: Carole

last: Ober

institute: The University of Chicago


title: scTCR-seq_P574

description:
10X Genomics
Real/RWC


title: scTCR-seq_P551

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, 85b2_4bcf


title: KO_CTL_AAV_Triceps_R4


title: scTCR-seq_P533

description:
10X Genomics
Real/RWC


title: WT_CTL_Liver_R1


title: KO_CTL_AAV_Triceps_R3


title: Control rep3


title: scTCR-seq_P523

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, cbb4_4a15


title: scTCR-seq_P528

description:
10X Genomics
Real/RWC


title: KO_CTL_AAV_Triceps_R2


title: Control rep1


title: scTCR-seq_P509

description:
10X Genomics
Real/RWC


title: KO_RAPA_AAV_Triceps_R2


title: TNBC tissue, replicate 4 [Spatial Transcriptome]

description:
YZL2
10x Spatial Transcriptome sequencing

value: breast tissue

value: triple negative breast cancer


title: KO_CTL_AAV_Triceps_R1


title: scTCR-seq_P498

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, 06ce_4533

value: female


title: KO_RAPA_Triceps_R3

value: RAPA


title: scTCR-seq_P481

description:
10X Genomics
Real/RWC


title: scTCR-seq_P399

description:
10X Genomics
Real/RWC


title: scTCR-seq_P394

description:
10X Genomics
Real/RWC


title: scTCR-seq_P390

description:
10X Genomics
Real/RWC


title: scTCR-seq_P483

description:
10X Genomics
Real/RWC


title: KO_RAPA_Triceps_R2


title: nasal_epithelial_cell, cd1c_49da


title: nasal_epithelial_cell, f75e_4388


title: KO_RAPA_Triceps_R1


title: scTCR-seq_P345

description:
10X Genomics
Real/RWC


title: scTCR-seq_P348

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, ba91_4656


title: scTCR-seq_P270

description:
10X Genomics
Real/RWC


title: scTCR-seq_P293

description:
10X Genomics
Real/RWC


title: KO_CTL_Triceps_R4


title: KO_CTL_Triceps_R3


title: scTCR-seq_P218

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, c009_4ead


title: scTCR-seq_P266

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, df3c_4959


title: scTCR-seq_P209

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, 7c18_465a


title: scTCR-seq_P269

description:
10X Genomics
Real/RWC


title: KO_CTL_Triceps_R2


title: nasal_epithelial_cell, 8228_4559


title: scTCR-seq_P172

description:
10X Genomics
Real/RWC


title: scTCR-seq_P105

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, 6660_423e

value: hispanic


title: scTCR-seq_P70

description:
10X Genomics
Real/RWC


title: scTCR-seq_P122

description:
10X Genomics
Real/RWC


title: WT_CTL_Triceps_R2

value: WT


title: nasal_epithelial_cell, 0d91_4a1c


title: C. auratus, diploid, male, replicate_5

city: Brno

first: Andrea

last: Šimková

address: Kamenice 5

institute: Masaryk University

data_processing:
A quality check of raw paired-end fastq reads was carried out by FastQC and their origin was categorized using BioBloomTools v2.3.4. The Illumina adapters clipping and quality trimming of raw fastq reads were performed using Trimmomatic v0.39 with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35. Trimmed RNA-Seq reads were mapped to the reference genome using STAR v2.7.3a as a splice-aware short read aligner and default parameters except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic. Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools – namely, RSeQC v4.0.0, Picard toolkit v2.25.6, and Qualimap v.2.2.2. All statistics were processed by MultiQC v1.10.1.
The genomic sequences of all collected samples were aligned to the reference genome utilizing the Burrows-Wheeler Aligner (BWA) software. Post alignment and germline variants were called using Strelka2 variant calling software, generating variant calls in VCF format which were further filtered to retain only high-confidence variants. These variants were then annotated using the reference annotation in GTF file. Subsequent data processing was carried out in R, where the variant tables were further refined and merged with sample information. A series of filtering steps were performed to ensure only variants with sufficient coverage and sample counts were retained for analysis. The filtered variant table was then reorganized and formatted for subsequent comparative analyses. Variants located on sex chromosomes were excluded for certain analyses to ensure accurate cross-species comparisons. The data were then restructured to compare SNP identity across species, generating similarity matrices and Venn diagrams to visualize the overlap of SNPs by species and ploidy levels.
The differential gene expression was calculated on the basis of the gene counts produced using featureCounts from the Subread package v2.0 and further analysed by Bioconductor package DESeq2 v1.34.0. Data generated by DESeq2 with independent filtering were selected for differential gene expression analysis to avoid potential false positive results. Differences in gene expression were considered significant on the basis of a cut-off of the adjusted p-value ≤ 0.05. GO term enrichment was analysed using David to retrieve Gene Ontology terms in the Biological process, Cellular Component and Molecular function categories, as well as KEGG pathways. Graphical representations of the GO enrichment were realized using R and Revigo. Reproduction-associated candidate genes were retrieved using the BlastKoala tool of KEGG, the BioMart tool of Ensembl, and published studies. GO terms enrichment was tested using Fisher’s exact test (α = 0.05) with false discovery rate (FDR) correction of the p-value. To interpret the biological functions of the DEGs, their mapping to the Gene Ontology (GO) and KEGG databases was performed to analyse pathway enrichment. In each of six fish groups associated with sexual reproduction and asexual males, significantly differently-expressed genes (DEGs) compared to the triploid asexual females of C. gibelio were selected on the basis of the following criteria: Basemean > 10, and a padj value < 0.05,. For KEGG pathway analysis, no filtering based on log2 fold change was applied. Gene functions were investigated using the biological databases Uniprot, KEGG, Zfin and GeneCards. PCA was performed using the DESeq2 R package. For PCA based on reproduction-associated genes, a set of 208 reproduction genes was selected using the BioMart tool of Ensembl.
Assembly: Carassius auratus genome (ASM336829v1) with Ensembl annotation (release 104)
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

organism: Carassius auratus

source_name: gonadal

extract_protocol:
Total RNA was isolated from the gonad tissue of each fish specimen. For extraction, PureLink® RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific) and on-column PureLink DNase treatment were used according to the manufacturer´s protocol. Reagent and buffer volumes were adjusted according to the weight of tissue entering the isolation process (30 mg on average). The final elution was performed using 100 µl of RNAse-free water in the first step and the primal eluate in the second step. The yield and concentration of RNA isolates were checked using a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) and Qubit RNA HS Assay Kit (Thermo Fisher Scientific). The quality and integrity of RNA were analysed using RNA 6000 Nano Kit on a 2100 Bioanalyser instrument (Agilent Technologies). All RNA isolates were normalized by dilution at a uniform concentration of 20 ng/µl with RNase-free water. They served as templates for DNA library preparation in twice the reaction volume recommended by the manufacturer.
All samples (RNA integrity number – RIN > 7) were used for DNA library preparation. 500ng of total RNA was used for mRNA enrichment using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®, and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) were used for library preparation, with 11 PCR cycles utilized for PCR enrichment. RNA fragmentation (13 minutes at 94°C) and the size selection conditions (a bead volume of 30 µl and 15 µl for the first and second bead selections, respectively) were further modified in the protocol. The quantification of DNA libraries was performed on a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific) using Qubit dsDNA HS Assay Kit, and quality and size control were performed on a 2100 Bioanalyser with DNA 1000 Kit (Agilent Technologies). Finally, amplicons were pooled in equimolar amounts. The final concentration of each library in the pool was 10 nM in the pool. Subsequently, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2, New England Biolabs) together with spike-in RNA were used for cDNA library preparation from total RNA. The quality of prepared cDNA libraries was evaluated using a Qubit fluorometer (Thermo Fisher). The quality of cDNA libraries was visualized by a 2100 Bioanalyser (Agilent), and the libraries were were finally sequenced by Macrogen Korea on Illumina HiSeq X (one lane) in a paired-end configuration producing 150 bp long reads.

value: gonadal

tag: ploidy

value: diploid


title: scTCR-seq_P64

description:
10X Genomics
Real/RWC


title: scTCR-seq_P33

description:
10X Genomics
Real/RWC


title: C. auratus, diploid, female, replicate_5


title: AB_10_3

city: Hangzhou

first: Bin

last: Yang

email: rayyangbin@163.com, binyang@zju.edu.cn

state: Zhejiang

address: No. 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
A total amount of 1 μg RNA per sample was used as input material to generate sequencing libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s recommendations.
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform (Illumina, San Diego, CA, USA), and 150 bp paired-end reads were generated.
Clean reads were obtained from the raw data by removing reads containing adapters, poly-N, and low-quality reads that did not pass the Illumina chastity filter using CASAVA (version 1.8, Illumina).
Assembly: High-quality reads were aligned to the sheep reference genome (Ovis aries v3.1) using TopHat2 software (v2.0.13).
Supplementary files format and content: Gene count were stored at the "total_count_d5-10.csv" file.

organism: Ovis aries

source_name: Abomasum epithelium, Day 10

extract_protocol: Immediately after slaughter, tissues of the rumen ventral sac, reticulum, omasum, and abomasum were removed from the muscle layer. Total RNA was extracted from the four stomach epithelia using a total RNA extraction kit.

value: Abomasum

tag: cell type

value: Epithelium

tag: time

value: Day 10


title: WT_CTL_Triceps_R1

tag: treatment

value: CTL


title: C. auratus, diploid, male, replicate_4

value: male


title: nasal_epithelial_cell, dbd7_4406

address: 920 E 58th Street, CLSC 501


title: nasal_epithelial_cell, 4666_4b42

value: multiple


title: KO_CTL_Triceps_R1

value: Agl KO


title: scTCR-seq_P591

description:
10X Genomics
IIT


title: scTCR-seq_P130

description:
10X Genomics
Real/RWC


title: AB_10_1


title: C. auratus, diploid, female, replicate_3


title: WT_CTL_Triceps_R3

value: Triceps


title: AB_5_3

source_name: Abomasum epithelium, Day 5

value: Day 5


title: AB_10_2


title: scTCR-seq_P590

description:
10X Genomics
IIT

value: lung


title: nasal_epithelial_cell, 6579_42f1


title: C. auratus, diploid, female, replicate_4


title: nasal_epithelial_cell, c08a_4789


title: scTCR-seq_P586

description:
10X Genomics
IIT


title: nasal_epithelial_cell, d8cb_4456


title: nasal_epithelial_cell, 4aea_49bc


title: nasal_epithelial_cell, 70d9_4bc6


title: C. auratus, diploid, female, replicate_2


title: nasal_epithelial_cell, 53cb_43c5


title: AB_5_1


title: C. auratus, diploid, male, replicate_2


title: OM_10_3

source_name: Omasum epithelium, Day 10

value: Omasum


title: scTCR-seq_P547

description:
10X Genomics
IIT


title: C. auratus, diploid, female, replicate_1

value: female


title: nasal_epithelial_cell, 99dd_417d


title: nasal_epithelial_cell, 8726_4d42


title: scTCR-seq_P531

description:
10X Genomics
IIT


title: nasal_epithelial_cell, aea1_4718


title: scTCR-seq_P589

description:
10X Genomics
IIT


title: C. auratus, diploid, male, replicate_1


title: scTCR-seq_P529

description:
10X Genomics
IIT


title: OM_10_2


title: nasal_epithelial_cell, 8ffe_41cd


title: OM_10_1


title: scTCR-seq_P519

description:
10X Genomics
IIT


title: AB_5_2


title: OM_5_2

source_name: Omasum epithelium, Day 5


title: nasal_epithelial_cell, 25e0_4e74


title: scTCR-seq_P438

description:
10X Genomics
IIT


title: C. auratus, diploid, male, replicate_3


title: scTCR-seq_P343

description:
10X Genomics
IIT


title: OM_5_3


title: OM_5_1


title: nasal_epithelial_cell, eeb4_44fd


title: scTCR-seq_P549

description:
10X Genomics
IIT


title: nasal_epithelial_cell, 6b35_49de


title: Patient1_normal

type: RNA

city: Suita

first: Tadashi

last: Oride

state: Osaka

address: 2-15 Yamadaoka

department: Obstetrics and Gynecology

institute: Osaka university

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 2 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: normal ovary

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNAs were extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's manual, and their quality was assessed using the NanoDrop 2000 (Thermo Scientific).

treatment_protocol: When patients underwent primary debulking surgery, specimens were extracted cleanly, washed twice with PBS, and frozen with liquid nitrogen as soon as possible.

tag: histology

value: normal ovary

tag: age

tag: Stage

value: IA


title: RE_10_3

source_name: Reticulum epithelium, Day 10

value: Reticulum


title: nasal_epithelial_cell, 1fc9_4979


title: Patient2_normal


title: ColonLP_myeloid_KO_aPD1_2

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave

department: Immunology&Pathology

institute: Washington University in St. Louis

description: polyA RNA

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8 software. tab-delimited file containing the raw reads count matrix
Assembly: GRCm38
Supplementary files format and content: filtered_feature_bc_matrix folder contents produced by the CellRanger pipelines, containing three files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz. For Bulk RNAseq all.genes_counts.tsv
Supplementary files format and content: all.genes_counts.tsv is a tab-delimited file containing the raw reads count matrix

source_name: Colon lamina propria

extract_protocol:
For scRNAseq: Using the Chromium Single Cell 3′ Reagent Kit v2 or v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing. For Bulk RNA seq: total tissue RNA was extracted using RNA easy mini kit. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
For scRNAseq: For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample. For bulk RNAseq: Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: Colon lamina propria

value: myeloid cells

tag: strain background

tag: genotype

tag: library type

value: RNA

tag: hto


title: scRNA-seq_P609

description:
10X Genomics
Real/RWC

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 6.1.2), employing GRCh38 as the reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 6.1.2) with the manufacturer-supplied human VDJ reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files


title: scRNA-seq_P603

description:
10X Genomics
Real/RWC


title: scRNA-seq_P605

description:
10X Genomics
Real/RWC


title: RE_10_1

value: Epithelium


title: Patient1_tumor

source_name: primary ovarian cancer

value: clear cell carcinoma


title: RE_10_2

value: Day 10


title: Patient2_tumor


title: RE_5_2

source_name: Reticulum epithelium, Day 5


title: ColonLP_myeloid_KO_aPD1_1

description: polyA RNA


title: nasal_epithelial_cell, 565d_44f8

tag: Sex

tag: proportionpositiveskinpricktests


title: nasal_epithelial_cell, 8ebc_4d6e

value: male

tag: plate

tag: ageindays

value: hispanic


title: scRNA-seq_P592

description:
10X Genomics
Real/RWC


title: RE_5_3


title: ColonLP_myeloid_WT_aPD1_2

description: polyA RNA

value: WT


title: ColonLP_myeloid_WT_aPD1_1

description: polyA RNA


title: scRNA-seq_P579

description:
10X Genomics
Real/RWC


title: nasal_epithelial_cell, 3880_42ec

tag: cohort (the year of sample recruitment)

tag: array


title: nasal_epithelial_cell, 06e7_4a83


title: scRNA-seq_P574

description:
10X Genomics
Real/RWC

tag: tissue


title: ColonLP_myeloid_KO_2

description: polyA RNA

tag: cell type


title: RE_5_1

tag: time


title: ColonLP_myeloid_KO_1

description: polyA RNA


title: ColonLP_myeloid_WT_2

description: polyA RNA


title: RU_10_2

source_name: Rumen epithelium, Day 10

value: Rumen


title: scRNA-seq_P533

description:
10X Genomics
Real/RWC


title: scRNA-seq_P551

description:
10X Genomics
Real/RWC


title: RU_10_3


title: nasal_epithelial_cell, c971_4ff3


title: scRNA-seq_P528

description:
10X Genomics
Real/RWC


title: MCA1956_CD45_Rg_4_3

description: HTO

library_source: other

molecule: protein

source_name: tumor

value: tumor

value: CD45+ cells

tag: treatment

value: Rg

value: HTO

value: TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody and TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody, TotalSeq™-B0303 anti-mouse Hashtag 4 Antibody


title: ColonLP_myeloid_WT_1

description: polyA RNA


title: Canine adipose-derived mesenchymal stem cells - biological replicate 12 - condition CHV-infected

city: Zagreb

first: Marina

last: Prišlin

address: Savska cesta 148

department: Virology Department

country: Croatia

institute: Croatian Veterinary Institute

description: Test group

data_processing:
Following data acquisition, normalization, and in-depth analysis were conducted using the specialized RT2 Profiler PCR Array Data Analysis software, accessible online at https://dataanalysis2.qiagen.com/pcr (accessed November 10th, 2023). For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, PGK1, ACTB. The statistical significance was calculated based on a Student’s t-test of the replicate 2^ (- Delta CT) values for each gene in the control and treatment groups. The software automatically appointed a fold change cutoff of 2.0, equal to log2Fold Change ± 1.0.
Fold Change worksheet reports test/control (CHV-infected/uninfected) ratios.

label: SYBR Green

organism: Canis lupus familiaris

source_name: Isolated and in vitro cultured adipose tissue cells

label_protocol: Genomic DNA elimination and complementary DNA synthesis from 800 ng of RNA was accomplished using the RT2 First Strand kit (Qiagen, Cat. 330401) as instructed by the manufacturer. Subsequently, a commercially available RT² Profiler™ PCR Array for Dog Mesenchymal Stem Cells (PAFD-082ZR, Qiagen) with SYBR Green-optimized primer assays (Qiagen, Cat. 330603) was applied, following the manufacturer's instructions for Rotor-Gene Q (Qiagen). The array featured primers targeting 84 genes, categorized as stemness markers, MSC-specific, MSC-associated, and MSC-differentiation genes associated with osteogenesis, adipogenesis, chondrogenesis, myogenesis, and tenogenesis.

growth_protocol: The extraction of cAD-MSCs was carried out within a two-hour window from sample collection. This process involved rinsing and cutting the adipose tissue with a scalpel, followed by enzymatic digestion using 0.5% collagenase type 1 (Gibco, Cat. 17100017). The obtained stromal vascular fraction was subsequently placed into T25 cell culture flasks (Nunc, Thermo Fisher Scientific) and cultured in basal media comprising 79% Dulbecco's Modified Eagle Medium with Low Glucose (DMEM Low Glucose) (Gibco, Cat. 31885049), 20% Fetal Bovine Serum (FBS) (Gibco; Cat. 1027010), and 1% Penicillin/Streptomycin (Sigma-Aldrich, Cat. P4333-100ML) at 37°C. Media was replaced after 24 hours, and when adherent cells reached 90% confluence, subculturing was performed using a solution of 0.05% Trypsin and 0.02% EDTA (Sigma-Aldrich, Cat. 59417C-500ML) until proliferation arrest was observed.

extract_protocol: Gene expression analysis using an RT-qPCR array was conducted following total RNA extraction in two conditions during in vitro culture, uninfected and canine herpesvirus (CHV) infected samples. The cAD-MSCs reached approximately 90% confluence in T75 cell culture flasks (Nunc, Thermo Fisher Scientific). Subsequently, the cells were detached using a cell scraper (Nunc, Thermo Fisher Scientific) and centrifuged at 235× g for 10 minutes. Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Cat. 74106) with 2M dithiothreitol (Sigma-Aldrich, Cat. 43815-1G), following the manufacturer's instructions. The extracted RNA was stored at -80°C until gene expression analysis.

tag: agent

value: canine herpesvirus


title: scRNA-seq_P523

description:
10X Genomics
Real/RWC

value: lung


title: Canine adipose-derived mesenchymal stem cells - biological replicate 11 - condition CHV-infected

description: Test group

value: female


title: nasal_epithelial_cell, c6a7_4e9f


title: scRNA-seq_P498

description:
10X Genomics
Real/RWC


title: scRNA-seq_P509

description:
10X Genomics
Real/RWC


title: RU_5_3

source_name: Rumen epithelium, Day 5

value: Day 5


title: RU_5_2


title: MCA1956_CD45_Rg_4_1

description: polyA RNA

value: RNA


title: AB_25_3

description: tissue transcriptomic data

data_processing:
Basecalls performed using CASAVA version 1.4.
TopHat2 (v2.0.13) with Bowtie2 (v2.3.3.1) was used to align the high-quality reads to the sheep reference genome (Ovis aries v3.1).
The BAM alignment files that were generated from TopHat2 were sorted by name and converted into SAM files using Samtools (v1.1).
HTSeq-count (v0.9.1) was used to count the number of reads per gene with the SAM files based on the annotation files.
Assembly: Ovis aries v3.1
Supplementary files format and content: Sample was represented by tab-delimited text files including raw counts of each gene for each sample.

source_name: Abomasum epithelium

growth_protocol: Normal feeding and management on commercial farm.

extract_protocol:
Total RNA were extracted using a total RNA extraction kit (Aidllab, Beijing, China) according to the instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All the RNA samples had integrity greater than 9.
RNA samples were subjected to cDNA library construction using the NEBNext UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations.

value: Abomasum epithelium

tag: age

value: 25 days of age

tag: gender

tag: strain

value: Hu sheep


title: MCA1956_CD45_Rg_3_2

description: HTO

tag: strain background

tag: genotype


title: Canine adipose-derived mesenchymal stem cells - biological replicate 8 - condition CHV-infected

description: Test group


title: nasal_epithelial_cell, 2aab_43f8

value: male


title: RU_5_1

value: Epithelium


title: Canine adipose-derived mesenchymal stem cells - biological replicate 9 - condition CHV-infected

description: Test group


title: Canine adipose-derived mesenchymal stem cells - biological replicate 10 - condition CHV-infected

description: Test group


title: MCA1956_CD45_Rg_3_1

description: polyA RNA

value: WT

tag: library type

tag: hto


title: scRNA-seq_P483

description:
10X Genomics
Real/RWC


title: scRNA-seq_P399

description:
10X Genomics
Real/RWC


title: AB_25_1

description: tissue transcriptomic data


title: RU_10_1

value: Rumen

value: Day 10


title: scRNA-seq_P394

description:
10X Genomics
Real/RWC


title: AB_25_2

description: tissue transcriptomic data


title: Canine adipose-derived mesenchymal stem cells - biological replicate 7 - condition CHV-infected

description: Test group

tag: Sex


title: Canine adipose-derived mesenchymal stem cells - biological replicate 6 - condition CHV-infected

description: Test group


title: MCA1956_CD45_CTRL_2_2

description: HTO

value: tumor

value: CD45+ cells

value: CTRL


title: Canine adipose-derived mesenchymal stem cells - biological replicate 5 - condition CHV-infected

description: Test group


title: MCA1956_CD45_CTRL_2_1

description: polyA RNA


title: MCA1956_CD45_Rg_4_2

description: polyA RNA

value: Rg


title: scRNA-seq_P390

description:
10X Genomics
Real/RWC


title: Canine adipose-derived mesenchymal stem cells - biological replicate 4 - condition CHV-infected

description: Test group

value: canine herpesvirus


title: MCA1956_CD45_CTRL_1_2

description: HTO

value: HTO

value: TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody and TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody, TotalSeq™-B0303 anti-mouse Hashtag 4 Antibody


title: OM_25_2

description: tissue transcriptomic data

source_name: Omasum epithelium

value: Omasum epithelium


title: MCA1956_CD45_CTRL_1

description: polyA RNA

value: RNA


title: scRNA-seq_P348

description:
10X Genomics
Real/RWC

source_name: lung

value: lung


title: Canine adipose-derived mesenchymal stem cells - biological replicate 3 - condition CHV-infected

description: Test group

value: female


title: scRNA-seq_P345

description:
10X Genomics
Real/RWC


title: OM_25_1

description: tissue transcriptomic data

value: 25 days of age

value: Hu sheep


title: scRNA-seq_P481

description:
10X Genomics
Real/RWC


title: Canine adipose-derived mesenchymal stem cells - biological replicate 1 - condition CHV-infected

description: Test group


title: RE_25_2

description: tissue transcriptomic data

source_name: Reticulum epithelium

value: Reticulum epithelium

value: male


title: scRNA-seq_P293

description:
10X Genomics
Real/RWC


title: RE_25_3

description: tissue transcriptomic data


title: Canine adipose-derived mesenchymal stem cells - biological replicate 2 - condition CHV-infected

description: Test group


title: OM_25_3

description: tissue transcriptomic data


title: Canine adipose-derived mesenchymal stem cells - biological replicate 11 - condition uninfected

description: Control Group


title: scRNA-seq_P266

description:
10X Genomics
Real/RWC


title: Canine adipose-derived mesenchymal stem cells - biological replicate 12 - condition uninfected

description: Control Group


title: scRNA-seq_P270

description:
10X Genomics
Real/RWC


title: RU_25_3

description: tissue transcriptomic data

source_name: Rumen epithelium

value: Rumen epithelium


title: TIL, ZT13, replicate 1

city: Genève

first: Christoph

last: Scheiermann

address: 1, rue Michel Servet

country: Switzerland

institute: UNIGE

description: 10X Genomics

data_processing:
Raw count matrices were generated with Cellranger v6.1.2 with mouse genome build mm10 as reference. Genes expressed in less than 20 cells were removed. Cells expressing less than 200 features, more than 7500 features, or more than 10% of mitochondrial genes were removed from further analysis.
Assembly: mm10
Supplementary files format and content: Rds file

source_name: Melanoma

extract_protocol:
Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer’s instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA.
Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer’s protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode.

treatment_protocol: non-treatted

value: Melanoma

tag: cell line

value: Tumor infiltrating leukocytes

value: WT

value: Female

value: 8-9 week

value: No


title: TIL, ZT19, replicate 1

description: 10X Genomics


title: RE_25_1

description: tissue transcriptomic data


title: RU_25_2

description: tissue transcriptomic data


title: TIL, ZT13, replicate 2

description: 10X Genomics


title: TIL, ZT19, replicate 2

description: 10X Genomics


title: TIL, ZT7, replicate 2

description: 10X Genomics


title: scRNA-seq_P223

description:
10X Genomics
Real/RWC


title: TIL, ZT7, replicate 1

description: 10X Genomics


title: Canine adipose-derived mesenchymal stem cells - biological replicate 10 - condition uninfected

description: Control Group


title: TIL, ZT1, replicate 2

description: 10X Genomics


title: Canine adipose-derived mesenchymal stem cells - biological replicate 9 - condition uninfected

description: Control Group


title: scRNA-seq_P218

description:
10X Genomics
Real/RWC


title: scRNA-seq_P269

description:
10X Genomics
Real/RWC


title: Canine adipose-derived mesenchymal stem cells - biological replicate 8 - condition uninfected

description: Control Group


title: AB_15_3

description: tissue transcriptomic data

value: Abomasum epithelium

value: 15 days of age


title: TIL, ZT1, replicate 1

description: 10X Genomics


title: scRNA-seq_P209

description:
10X Genomics
Real/RWC


title: AB_15_2

description: tissue transcriptomic data


title: Canine adipose-derived mesenchymal stem cells - biological replicate 7 - condition uninfected

description: Control Group


title: scRNA-seq_P172

description:
10X Genomics
Real/RWC